Dosage compensation is the process by which the expression of X-linked genes is altered in one sex to counterbalance the difference in X-chromosome and autosome number in the heterogametic sex. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to equalize expression levels of X- linked genes in males accompanies Y-chromosome degeneration, thus driving the evolution of dosage compensation. Drosophila miranda - a species for which we recently generated a de novo genome sequence assembly - has three sex chromosomes of different age and at different stages of transition from ordinary autosomes into heteromorphic sex chromosomes. Specifically, X-L is the ancestral sex chromosome of the genus Drosophila and >60MY old, X-R is shared by members of the D. pseudoobscura subgroup and >10MY old, while its neo-sex chromosome (about 1MY old) still largely resembles an autosome, but the neo-X is evolving partial dosage compensation. D. miranda therefore provides a unique system to study the evolution of dosage compensation in action using a comparative and functional genomics approach. We will use ChIP-seq techniques together with whole-genome population analysis to functionally characterize the targeting of the dosage compensation complex to the X chromosome, and how it evolves. PUBLIC HEALTH RELEVANCE: Expression networks are often fine-tuned, and chromosomal aneuploidy and changes in gene dosage can disturb the overall balance of gene expression networks, and are associated with several known human diseases and birth defects (Down syndrome results from an extra copy of Chromosome 21), and chromosomal aneuploidies are also frequent in cancer cells. Sex chromosomes, in contrast, provide systems of naturally occurring aneuploidy, with females having two X chromosomes and males having one X and a Y, resulting in X monosomy in males, and unique gene regulation strategies have evolved to compensate for this gene-dose deficiency in males. We will use the model species Drosophila to investigate evolutionary and functional aspects of dosage compensation, which will help to understand the effects of aneuploidy on gene expression and the mechanisms that alleviate aneuploidy-induced expression imbalances of the genome.